Harry, I think you are probably right, although it depends on the reader of course. Certainly Kobo has chosen to override a 'body' choice; I'm not sure what my new Sony T1 does yet.
In my opinion, having the publisher force a font choice on the user removes one of the nicer features of ebooks. I think the user, not the publisher and not the ereader maker, should have the choice of body font. I'm a hopeless idealist.

Kobo has created a serious bug and they refuse to fix it. Most publishers and people who create ePub with embedded fonts use the body style to put the main font-family declaration. That won't work on any Kobo eink reader and it's a bug they've been told about and refuse to fix. Kobo users are likely to get a lesser reading experience when the ePub has an embedded font.

The new Star Wars eBooks all have an embedded font and yet Kobo will not display it at all.